/*
 * Jalview - A Sequence Alignment Editor and Viewer
 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
 */

package jalview.appletgui;

import java.util.*;

import java.awt.*;
import java.awt.event.*;

import jalview.datamodel.*;
import jalview.jbappletgui.*;

public class Finder
    extends GFinder
{
  AlignViewport av;
  AlignmentPanel ap;
  Frame frame;
  SuperGroup searchGroup;
  Vector searchResults;

  int seqIndex = 0;
  int resIndex = 0;
  public Finder(final AlignmentPanel ap)
  {
    this.av = ap.av;
    this.ap = ap;
    frame = new Frame();
    frame.add(this);
    jalview.bin.JalviewLite.addFrame(frame, "Find", 340, 120);
    frame.repaint();
    frame.addWindowListener(new WindowAdapter()
    {
      public void windowClosing(WindowEvent evt)
      {
        ap.highlightSearchResults(null);
      }
    });
  }

  public void textfield_actionPerformed(ActionEvent e)
  {
    doSearch(false);
  }

  public void findNext_actionPerformed(ActionEvent e)
  {
    doSearch(false);
  }

  public void findAll_actionPerformed(ActionEvent e)
  {
    resIndex = 0;
    seqIndex = 0;
    doSearch(true);
  }

  public void cancel_actionPerformed(ActionEvent e)
  {
    try
    {
      // if allResults is null, this effectively switches displaySearch flag in seqCanvas
      ap.highlightSearchResults(null);
      ap.idPanel.highlightSearchResults(null);
      // frame.setClosed(true);
    }
    catch (Exception ex)
    {}
  }

  public void createNewGroup_actionPerformed(ActionEvent e)
  {
    Color[] newColors = new Color[24];
    for (int i = 0; i < 24; i++)
    {
      newColors[i] = new Color(60, 160, 115);
    }

    jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
        newColors);
    String searchString = textfield.getText();

    searchGroup = new SuperGroup(searchString, ucs, true, true, false);

    for (int i = 0; i < searchResults.size(); i += 3)
    {
      // its possible edits may have occurred since search was performed
      // account for this here

      SequenceI seq = av.alignment.getSequenceAt(Integer.parseInt(searchResults.
          elementAt(i).toString()));
      int startRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i +
          1).toString())) - 1;
      int endRes = seq.findIndex(Integer.parseInt(searchResults.elementAt(i + 2).
                                                  toString())) - 1;

      SequenceGroup sg = new SequenceGroup(searchString, ucs, true, true, false,
                                           startRes, endRes);
      sg.addSequence(seq, false);
      av.alignment.addGroup(sg);
      searchGroup.addGroup(sg);

    }

    ap.av.alignment.addSuperGroup(searchGroup);
    ap.highlightSearchResults(null);
  }

  void doSearch(boolean findAll)
  {
    createNewGroup.setEnabled(false);

    String searchString = textfield.getText().toUpperCase();

    com.stevesoft.pat.Regex regex = new com.stevesoft.pat.Regex(searchString);

    searchResults = new Vector();
    int[] allResults = null;

    Sequence seq;
    String item = null;
    boolean found = false;

    ////// is the searchString a residue number?
    try
    {
      int res = Integer.parseInt(searchString);
      found = true;

      if (av.getSelectionGroup() == null || av.getSelectionGroup().getSize() < 1)
      {
        seq = (Sequence) av.getAlignment().getSequenceAt(0);
      }
      else
      {
        seq = (Sequence) (av.getSelectionGroup().getSequenceAt(0));
      }

      searchResults.addElement(Integer.toString(av.getAlignment().findIndex(seq)));
      searchResults.addElement(String.valueOf(res));
      searchResults.addElement(String.valueOf(res));

    }
    catch (NumberFormatException ex)
    {}
    ///////////////////////////////////////////////


    int end = av.alignment.getHeight();

    SequenceGroup selection = av.getSelectionGroup();
    if (selection != null)
    {
      if (selection.getSize() < 1 ||
          (selection.getEndRes() - selection.getStartRes() < 2))
      {
        selection = null;
      }
    }

    while (!found && seqIndex < end)
    {
      seq = (Sequence) av.alignment.getSequenceAt(seqIndex);

      if (selection != null && !selection.sequences.contains(seq))
      {
        seqIndex++;
        resIndex = 0;
        continue;
      }

      item = seq.getSequence().toUpperCase();

      if (selection != null && selection.getEndRes() < av.alignment.getWidth())
      {
        item = item.substring(0, selection.getEndRes() + 1);
      }

      ///Shall we ignore gaps????
      StringBuffer noGaps = new StringBuffer();
      int insertCount = 0;
      Vector spaces = new Vector();

      for (int j = 0; j < item.length(); j++)
      {

        if (!jalview.util.Comparison.isGap(item.charAt(j)))
        {
          noGaps.append(item.charAt(j));
          spaces.addElement(new Integer(insertCount));
        }
        else
        {
          insertCount++;
        }
      }

      for (int r = resIndex; r < noGaps.length(); r++)
      {

        if (regex.searchFrom(noGaps.toString(), r))
        {
          resIndex = regex.matchedFrom();
          if (selection != null &&
              (resIndex + Integer.parseInt(spaces.elementAt(resIndex).toString())) <
              selection.getStartRes())
          {
            continue;
          }

          searchResults.addElement(Integer.toString(seqIndex));
          int sres = seq.findPosition(resIndex +
                                      Integer.parseInt(spaces.
              elementAt(resIndex).toString()));
          int eres = seq.findPosition(regex.matchedTo() - 1 +
                                      Integer.parseInt(
                                      spaces.elementAt(regex.matchedTo() - 1).
                                      toString()));
          searchResults.addElement(sres + "");
          searchResults.addElement(eres + "");

          if (!findAll)
          {
            // thats enough, break and display the result
            found = true;
            resIndex++;
            break;
          }

          r = resIndex;
        }
      }
      if (!found)
      {
        seqIndex++;
        resIndex = 0;
      }
    }

    Vector idMatch = new Vector();
    for (int id = 0; id < av.alignment.getHeight(); id++)
    {
      if (regex.search(av.alignment.getSequenceAt(id).getName()))
      {
        idMatch.addElement(av.alignment.getSequenceAt(id));
      }
    }

    if (searchResults.size() == 0 && idMatch.size() > 0)
    {
      ap.idPanel.highlightSearchResults(idMatch);
    }

    if (searchResults.size() > 0)
    {
      allResults = new int[searchResults.size()];
      for (int i = 0; i < searchResults.size(); i++)
      {
        allResults[i] = Integer.parseInt(searchResults.elementAt(i).toString());
      }

      createNewGroup.setEnabled(true);
    }
    else
    {
      resIndex = 0;
      seqIndex = 0;
    }

    // if allResults is null, this effectively switches displaySearch flag in seqCanvas
    ap.highlightSearchResults(allResults);

    if (findAll)
    {
      String message = (searchResults.size() / 3) + " matches found.";
      System.out.println(message);
    }

  }

}